4.5SI RNA genes and the role of their 5′-flanking sequences in the gene transcription

4.5SI RNA is a small nuclear RNA synthesized by RNA polymerase III and detected in rodents of only four families. Hundreds of copies of this RNA retropseudogenes are interspersed throughout the mouse (Mus musculus) and rat (Rattus norvegicus) genomes. We found a single locus containing 4.5SI RNA genes in the genomes of these rodents. The locus harbors three genes and occupies 80 kb on M. musculus chromosome 6 and 44 kb on R. norvegicus chromosome 4. Two long duplications seem to have taken place during evolution of this locus. Two mouse 4.5SI RNA genes were used for a study of the role of 5′-flanking sequences in transcription in vitro and ex vivo. We found that removal of these DNA sequences resulted in a dramatic reduction of transcription though an internal promoter for RNA polymerase III was preserved in 4.5SI RNA genes. Thus, 5′-flanking sequences (from − 1 to − 90) containing conserved regions are important for 4.5SI RNA gene expression.